


Agonizing Beginnings

by Nat (NotSoNeatNat), NotSoNeatNat



Category: Shadowhunters (TV), The Mortal Instruments Series - Cassandra Clare
Genre: Demons, Evil, Gay, Hurt Alec Lightwood, Hurt Magnus Bane, Hurt/Comfort, Kidnapping, M/M, Malec, New York Shadowhunter Institute, Original Character(s), Parabatai, Temporary Character Death, Torture
Language: English
Status: In-Progress
Published: 2020-12-06
Updated: 2020-12-26
Packaged: 2021-03-09 20:34:09
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings, Graphic Depictions Of Violence, Major Character Death, No Archive Warnings Apply
Chapters: 9
Words: 8,252
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/27922330
Author URL: https://archiveofourown.org/users/NotSoNeatNat/pseuds/Nat, https://archiveofourown.org/users/NotSoNeatNat/pseuds/NotSoNeatNat
Summary: Alec Lightwood and Magnus Bane lived happily in their Brooklyn loft with their adopted warlock son Max, now 4 years old. Being a mighty warlock/Nephilim couple has the potential to place their lives in great danger. Evil is afoot in New York City, seeking the powerful pair for their demonic experiments. Alec suffers greatly while Magnus watches their captors use his angel blood for their nefarious purposes.
Relationships: Magnus Bane/Alec Lightwood
Comments: 9
Kudos: 34





	1. 1: Hey Magnus?

**Author's Note:**

> I do not own The Mortal Instruments universe or its characters, that goes to the wonderful Cassandra Clare.

It was a crispy autumn afternoon in Brooklyn NY, small tufts of white decorate the sky while the sun shines brightly without an overbearing heat. In one particular loft on one particular street, Alec Lightwood-Bane attempts to get his 4 year old son to fly down from the ceiling. Max is a very spunky warlock kid and uses his magical power to play accordingly. The blue child giggled happily as he floated beyond his father's long reach. Alec was a great dad, but Magnus was much better at dealing with Max's more warlock-y behaviors.

"Hey Magnus?" Alec called in a defeated tone to his husband in the other room.

"Yes Alexander?" The sparkly warlock cooed in reply.

"He's doing it again." Responds Alec. "I swear, every time you leave the room he goes up there just to push my buttons."

Magnus then waltzes his way into the living room, not without his trademarked swagger, and spoke to his son, "Awww, they grow up so fast" he said with a smirk and Alec cast him an unamused look and suave as usual Magnus teased, "I'm sure he only does it because you look so cute when you're on your last nerve", before his husband could scold him.

Even after all of his years with Magnus, the compliment still gave Alec a slight blush and in his flustered state he only managed to sputter out, "Just help me get him down."

**_A/N :_** _**Hey y'all! I know this first chapter is really short but the others will be longer. This is my first time writing a fanfic so I will take constructive criticism if you have any tips or suggestions. I have a pretty**_ _ **clear idea of what I want the main plot to be for this fic, but I don't think it'll be that many chapters so if y'all have ideas of what I could add on after I run out or if you have other story suggestions, put it in the comments. Anyways, thanks so much for taking the time to read my work! I hope you enjoy it!**_

**_~Nat_ **


	2. 2: Old Habits

**Summary for the Chapter:**

> Alec is restless as head of the institute.

It was a new day and after giving Max a kiss on the forehead while he slept in and leaving the pot of coffee on for Magnus along with some fresh flowers on the table, Alec left for work. Alec Lightwood-Bane was head of the New York shadowhunters institute and everyday he liked to get there a bit early so he could get in some training before the real work began. Alec enjoyed being head of the institute, but it was mostly a desk job and Alec missed being out in the field. It was still dark in the training room when he arrived, but Alec didn't bother to turn the lights on.

After an hour of vigorous exercise someone else came into the training room and flicked the light on. Alec turned to find Jace, his parabatai, smirking his normal smirk at him.

"Feeling restless?" Jace called out to his brother.

"No, just getting a little workout in" Alec replied evenly while going back to punching the dummy in front of him. But Jace called Alec's bluff.

"You're forgetting that we share feelings." Jace scoffed. "I know there's something bothering you." His voice held a sincere tone that showed Alec the true brotherly concern Jace was feeling. Alec sighed, knowing that he wasn't about to let this go, he would have to talk eventually.

"I haven't been out in the field in months, I miss being in the fight, I feel like I just sit around doing paperwork all day, every day. I'm sick of this job." Alec confessed and Jace's smirk reappeared.

"You, dear brother, are having a midlife crisis." He said.

"I'm 25." Alec pointed out with a confused frown.

"I'm just giving you a hard time." Alec's brow furrowed further so Jace continued. "Look, you're the most heroic shadowhunter in the entire institute, aside from me of course. The work you do every day saves lives, your strategy and guidance leads every single one of us to being better shadowhunters." Jace walked towards Alec. "It doesn't matter whether you're at a desk or holding your bow, you're at the front of this fight, and fighting harder than anybody else." Jace placed a reassuring hand on his parabatai's shoulder as Alec finally met his eyes.

"I know you're right. But I just miss it. The thrill of the hunt. The rush of defeating evil." Alec sighed. Alec's words gave Jace an idea.

"I know what you should do,"

"What?"

"Just go out on patrol tonight."

"You say that like it's easy. I'm head of the institute Jace."

"Exactly, you're in charge, no one is going to stop you"

"Jace, I have work to do, I can't just ditch."

"I'll do it for you tonight and you can take my spot on patrol." Alec raised a brow. "What? You can trust me! Remember, I was offered this position first." Alec huffed in protest. "Hey, I'm the one offering you a favor."

"And I appreciate the offer, but no matter how much I might want to go, I can't just abandon my duty." Alec said with determination.

"Okay. I respect that. Oh yeah, I just remembered, Magnus is joining us tonight on patrol again."

"I'm going." Alec quickly changed his mind.

"Mmm hmm, that's what I thought." Jace commented smugly.

"Oh, while I'm gone I'll need you to oversee some correspondence with the Seelie queen." It was Alec's turn to smirk as Jace swallowed the rising lump in his throat. He regained his composure almost instantly, anyone but Alec wouldn't have been able to tell there was ever anything wrong.

"Sure bud. Anything for you Alec. I gotta get you out of this slump." Jace said, reapplying his cool guy coating. With that Alec gave Jace a brotherly punch in the arm and left the training room to shower off the salty sweat that had collected from the activities of the past hour. As he was exiting, he thought he heard something moving by the window. He looked up to find nothing. Still cautious, he continued on his previous path.

After properly grooming himself for the day Alec stepped into his office and frowned at the large stack of papers that sat atop his large wooden desk in the center of the warmly rustic room. He walked over to his large leather swivel chair and sat down, getting to work. It was hours later and he had gotten through nearly three quarters of the stack when Isabelle knocked on his door.

"Yes?" Alec said as the door was opened. "Oh hey Izzy, what's up?"

"Hey big bro," She said with a playful grin, "I heard you're playing hooky tonight!" Alec tensed, "Reeeelaaaxxx Alec, it's not like I'm gonna tell dad. I'm actually excited! It's been forever since we've gone on a hunt together." Alec's shoulders loosened.

"I'm looking forward to it too, I've been cooped up here for too long. I just hope Jace will be okay running the institute while I'm gone." He talked back uncertainly.

"Jace will be just fine, he's a natural at everything." Seeing Alec's unimpressed look she added, "Plus, Jace would never let you down." At that Alec seemed more at ease. Though he did worry about the institute, he had trust in his parabatai.

It was finally time for Alec to prepare for patrol, he was excited. It had been so long since he had last dawned the shadowhunter gear, his old armor still hugged his body in all the right places, earning him a whistle from somewhere behind him. He whipped around with a scowl on his face only to find his husband, Magnus. Upon seeing his love his expression softened and instead of Alec being upset at the sound of someone ogling him he struck a sexy pose for his husband who then proceeded to give him a peck on the lips before summoning Alec's bow for him from thin air along with his quiver of arrows. Alec gave Magnus another kiss while he grabbed his bow from Magnus. When they parted Magnus couldn't help but giggle at the sight of Alec's dopey grin.

"You excited?" Magnus asked, already knowing the answer.

"Very." Alec responded.

**_A/N:_** **_Hey y'all! This update is a bit longer than the first one, this will probably be the benchmark for chapter length._** **_Right now we're still in the exposition but rest assured, the next chapter will be when the drama starts. oOOooOoOOooh*spooky noise* :P Anyways, I hope you liked this chapter! If you have any tips or suggestions, or if I misspell things or write incoherent sentences let me know. And positive feedback is always appreciated! Hope y'all are doing well in these trying times._**

**_~Nat_ **


	3. 3: The Hunt

**Summary for the Chapter:**

> Alec goes out in the field for the first time in months on patrol with Magnus, Izzy, Clary, and Simon.

The sun had just gone down and the shadowhunters began their patrol. Alec was practically bouncing with excitement, he was on patrol with Izzy, Clary, Simon, and Magnus. They stalked quietly down the streets of Manhattan searching for demons, but after about 3 hours, none had appeared.

"Sorry Alec, demonic activity has been pretty low lately. We probably won't get any action tonight." Simon, ever the empath, said.

"No, it's okay, no demons is a good thing..." Alec responded but his tone was distracted and his head was on a swivel.

"Alec? What is it?" Izzy asked her brother.

"I don't know..." He replied, "Just a bad feeling." A low rumbling sound could be heard in the distance and started to pierce the loud hubbub of city streets, as it grew nearer sharp shrieks could be heard over the beating of... wings? They all turned in the direction of the strange noise and saw a swarm of harpyia demons flying their way. The shadowhunters immediately took on their fighting stances. Alec and Simon attacked first with their arrows while the demons were still approaching, keeping most of the deathly cloud at bay. Magnus was at Alec's side holding the hoard back until too many of the rag-like winged demons had made it through the relentless barrage of fire and he turned to short range combat. Izzy and Clary were behind them, Izzy's whip and Clary's dual kindjals slashing demons down left and right meanwhile Magnus had moved slightly away from the group so he could use some more powerful magic.

Preoccupied with cutting down 4 other demons simultaneously, Izzy was left defenseless against the fifth harpyia that swooped down and clawed at her with its sharp talons. It was only able to create a small gash along her arm before it was struck by one of Simon's arrows. Seeing she was hurt, Simon ran to Izzy's side. At that moment Alec turned to see a large demon diving out of the sky toward the venerable couple, who were to occupied with each other's safety to actually be paying attention to it.

"Look out!" Alec shouted at the two before loosing an arrow that would bury itself in the lifeless eye socket of the demon's skull.

Alec's shout had captured Magnus's attention and he spun to catch a glimpse of the situation. The seconds after Alec released that arrow felt like hours to Magnus. He screamed out his husband's name as a massive harpyia approached Alec from behind and clamped its massive jaws, with a seemingly endless number of dagger-like teeth, down on the shadowhunter's shoulder. Magnus saw it all unravel in ultra-slow motion, Alec met his gaze for a split second in confusion and then went pale with shock before his face twisted in anguish. The worst part though, was the scream. The cry of pain that erupted from Alec's bleeding figure broke Magnus in ways he had never thought he could break. The Earth shattering roar burned in Alec's lungs but that pain was miniscule compared to what he was feeling. The demon proceeded to flap its wings in a dramatic fashion before taking off into the sky with Alec still in its hold, desperately trying to free himself and calling for the aid of his friends.

"ALEC!" Magnus shouted panicked, he looked to Simon, who was much closer, "WHAT ARE YOU DOING SHOOT IT DOWN!"

"Oh right!" Simon had almost forgotten his bow in his state of fear. When he raised it his hands shook with fear and in his hesitation Alec and the demon were out of range. He lowered the bow and turned back to Magnus who's eyes held so much fear, worry, and anger.

"ALEC!" He screamed, beginning to run in the direction that the beast had taken him. "ALEC!" He was stopped by Izzy.

"Magnus, running off after Alec isn't going to help him now. We need to come up with a plan." Magnus looked into Isabelle's eyes, his own growing in they're portrayal of fear and worry. "We'll find him Magnus, you'll get him back." Izzy said with uncertainty but determination.

"HOW!?!" Magnus replied desperately, "If you didn't notice, all of the other demons are gone now! Which means they only came for Alec! They're gonna kill him!" Magnus worried when Simon butted in,

"That doesn't make sense, if they wanted to kill him, they would've just killed him, they took him for some other reason." Magnus's face paled even more and Simon realized what he just said. Finally Clary spoke up,

"We've gotta get Jace." She said with a swallow.

 ** _A/N:_** **_Hey y'all! Told ya this is where it starts gettin' spicy! It'll only grow from here. Anyways, I hope you guys are having a good day, thanks for reading my story!_**

**_~Nat_ **


	4. 4: What'd'ya mean gone!?

**Summary for the Chapter:**

> Back at the institute, the others have to tell Jace about what happened to Alec, meanwhile, Magnus is coming undone.

"WHAT HAPPENED!?!" Jace roared as he saw his friends walk back inside the institute, he frantically searched for Alec among them. "Where's Alec? Something's wrong with our parabatai bond, a little bit ago there was this flash of white hot pain and now I can't feel him at all." Upon hearing this most unencouraging information from Jace, Magnus felt as if he would throw up.

"What do you mean you can't feel him? Your rune's not gone, is it?" Isabelle fought hard but she couldn't keep the slight waver out of her voice. Her eyes, locked on Jace's, were frantically searching for a thread of hope to hang onto. He slightly eased the group's worry when he pulled his shirt down, revealing the skin of his left shoulder, still baring the prominent rune.

"Thank the Angel." Izzy exhales. Jace was growing more concerned and irritated by the second.

"You still haven't answered my question, where's Alec?" The others looked between themselves, silently deciding between the four of them that it would be Clary to tell Jace the news. She spoke gently, stepping forward to place a hand on his shoulder.

"He was taken by a swarm of harpyia demons after saving Izzy and Simon from a demon that got the drop on them. We don't know where he is." Although Jace wasn't stupid and had figured out that that was most likely what had happened, hearing it be said made a pit in his stomach that felt bottomless.

"Has anyone tried tracking him?" Jace asked.

"No," Simon responded, "We came back here hoping to find an object we could use." Jace turned on his heel, the others in tow, towards Alec's office. Once they reached it Jace promptly grabbed the photo of Magnus, Max, and Alec from the desk and drew a tracking rune on the back of his hand. After a few seconds, he let out a dissatisfied growl and slammed the picture back down.

"It's not working!"

"Give it to me," Magnus said in a serious voice, "warlock tracking is stronger." Jace handed the picture over. Magnus took it in his hands and closed his eyes, performing the tracking spell. After 2 minutes of silence Magnus dropped to his knees on the floor, finally letting tears fall. "I can't find him." He said in a soft, broken voice, the cracks in which showed the ultimate sorrow that he was feeling.

"Papa!" Max came running into the room with Maryse not far behind. He wrapped his arms around his papa and asked, "Where's Daddy?" Magnus put on a fake smile for his son.

"He'll be back in a little bit." Magnus told him, trying his best to make a brave face so Max wouldn't detect the lie. Maryse however couldn't be fooled and saw the looks on everyone's faces and decided that it would e best to get Max out of there and let them work to rescue her son. She gave the group a look over her shoulder as she was exiting with Max in her arms that said that she wanted an explanation later.

"What are we going to do?" Izzy asked. Everyone remained quiet. The only audible sound was Magnus's light sobs. Deciding to give Magnus some time to collect himself, Izzy, Jace, and Simon left to make a plan in the control room.

Magnus pulled himself across the floor to lean against Alec's desk. He had stopped crying. Magnus was so heartbroken he couldn't cry any more. It was all he could do to breathe and he knew that Alec wasn't even dead. 

All of a sudden, Magnus felt a familiar sort of vibration in the air. He reached out his hand to retrieve the fire message.

_Dear Magnus Lightwood-Bane,_

_You must be having quite the day old friend. I have your beloved. He's not the friendliest. I would've thought if you were ever to get married they'd at least be someone with manners. Anyways, I'm back to my ways and unless you come rescue him, your dear Alec is going to be my latest experiment. And I am rather out of practice, considering what you did to me, and this one might not go well. If you want your sweetheart back in one piece, you'll find us where my dear brother was betrayed by his own beloved for 15 years._

_Tata for now darling,_

_Clementine Morgenstern_

_P.S. Come alone or he dies. ;)_

Magnus wasn't stupid. He knew it was a trap. He wasn't planning on going alone. But right when he got the the entrance of the control room he heard someone cry out in pain. It was Jace. He was on the floor, clutching his parabatai rune. Alec was being tortured. Magnus could no longer risk it. He had to go alone. Clementine was not messing around. When the noises stopped Jace said, "He's blocking me out."

"What does that mean?" Clary asked.

"He's not letting me share his pain." Jace replied.

"Classic Alec," Izzy's tears escaped her eyes and betrayed her will. "even when he's been kidnapped and tortured, he's still worried about everybody else." She had the smallest of smiles, proud of how strong and selfless her big brother was.

Without being seen by the others, Magnus left to get Alec back. He was strong enough on his own. 

He would have to be.


	5. 5: Rendezvous

Alec blinked his eyes open to a bright light shining in his face, he looked around, not able to make out anything more that three feet away. He wasn't sure when he had fallen unconscious. He must've passed out from the pain. Pain? Oh, that's right, he had been bitten in the shoulder and carried off by a demon. But where was the pain now? He looked to where there should've been a massive wound only to find the remains of a iratze rune. He moved to trace the faint scar of jaw marks that stretched from his shoulder to the middle of his chest but when he tried he found himself restrained. Finally taking note of his surroundings, Alec found himself affixed to a metal table with steel cuffs around his wrists and ankles. The table was at an angle so that he was almost standing upright. He let out a puff of air that hung in the cold air like a cloud, Alec suddenly realized he was freezing cold. He was wearing nothing but his tattered and blood soaked pants, his bare back was exposed to the painfully icy surface of the metal. 

Alec heard footsteps coming from behind. He turned to look but was stopped by his bindings. The figure made a wide circle around Alec, staying out of the light so he could not see their face. When they were directly in front of him they stopped.

"Well look who's awake!" An unexpectedly cheerful female voice called out, echoing around the apparently large stone room. "Alec Lightwood-Bane. I've heard so much about you." She paused, waiting for Alec to say something, when she got no reply she huffed, "I guess they did say you were the quiet type. But seriously? No 'where am I'? No 'who are you'? Not even a 'why are you doing this'?" She said in mock suffering, "What's a bad guy got to do around here to get a little repartee around here?" 

"Fine," Alec decided getting some answers was step one. "Who are you and why the hell am I here?"

"Ah he speaks!" Her voice was disturbingly light. "Well my dear, my name is Clementine Morgenstern. And as for why you're here, well, that's a much longer story that I'd prefer to tell with the help of another guest who should be arriving soon. Your beloved husband won't be able to play by the Clave's rules for long." Alec thrashed against his restraints rubbing his skin raw trying to throttle the woman.

"YOU STAY AWAY FROM MAGNUS!" Alec yelled to his captor.

"Tsk tsk dear, you've got it all wrong." Her voice suddenly dropped to a much darker timbre. "It's Magnus Bane who should've stayed away from me." And with that she stepped into the bright light and Alec could see her light hair and dark eyes and a face he recognized all too well.

Valentine.

Alec had only seconds to ponder this before she was swinging her fist at his face, splitting his lip and knocking him out.

****************************

Magnus couldn't bare to think what would happen if he failed. He had only just managed to defeat Clementine the first time, and now she had Alec. What would she do to him? There was no telling. He evaded passing shadowhunters and made his way out of the institute where he could portal. He knew exactly where Clementine wanted to meet him and he opened the magical pathway to the childhood apartment of Clary Fray.

Upon first entrance to the home it was in the same ruin it was left from the last demon fight. Magnus listened closely before calling out. "Clementine? I'm here. Give Alec back. You can have me if you want. Just don't hurt him." He pleaded to the empty room. Suddenly he felt a chill go up his spine and a voice in his head,

_I will have whatever I want dear._

That's when five forsaken burst through the nearest wall, all running for Magnus. He turned on his heel and ran out of the apartment. Attempting to go down the stairs he found an army of Moloch demons, dripping in oil and ichor, flooding the lower level of the building. There was only one way out.

Fight.

Magnus burst into action, firing his magic at the demons and sending them back to their own realm. He was making progress on the sea of demons below him but in doing so was not paying close enough attention to the forsaken that had followed him out of the apartment. Turning so he could keep both forces at bay he neglected to spot the Shax demon lurking behind him. It grabbed Magnus by the neck with its pincers and squeezed until his vision went black and his body limp and proceeded to drag his unconscious form through the tunnel it had dug through the building's floor.

When Magnus awoke he was on his knees, hanging by his wrists chained to a wet stone wall in a dark room. The only light directed his eyes to an unconscious figure bound to a metal table surrounded by science equipment.

"Alec!" Magnus shouted, getting to his feet. "Alexander!" Alec stirred and slowly opened his eyes.

"Magnus?" He was puzzled, then his expression switched to fear. "Magnus no! You can't be here, it's not safe."

"Obviously it's not safe! That's why I came to get you!" Magnus replied, frustrated with his self sacrificing husband. That's when a voice all to familiar to Magnus pierced their moment.

"I hate to break up such a tender reunion between lovers, but I have a little reunion of my own. Hey Mags! Long time no see!" 


	6. 6: Agony

Alec was confused. "You guys know each other?" He asked.

"Go on dear, I'll let you tell him." Clementine smiled an evil smile. As Magnus took a deep breath in as he prepared to deliver the last of the author's exposition.

"Clementine Morgenstern is the older, sociopathic, sister of Valentine Morgenstern." Magnus spat. "Before the uprising, before the circle, she had her own radical outlook. Unlike her brother, whose goal was to completely wipe out the downworld, she sought to merge with them to create a superior breed of shadowhunter that would rule over the mundane and shadow worlds. She subjected shadowhunters and downworlders alike to her cruel experiments. Most did not survive. She was unable to be stopped by the shadowhunters sent after her so the clave called me in to do a little favor. I sent her to the void."

"That's right Maggie!" Clementine cooed. "And even though I made it out, whoop-dee-doo, and my time in the void allowed me to make friends with an army of demons that are now under my control, you're still gonna have to pay for what you did."

"Fine," Magnus said. "Make me pay. Just let Alec go." Clementine clicked her tongue in disapproval.

"Ummmmmmmmmmmmm......No<3" She seemed proud of herself. "You see, I'm gonna make _you_ pay by making," she pointed to Alec, " _him_ pay."

"No! He has nothing to do with this!" Magnus begged.

"And I might as well start again where my plan left off..." Clementine chortled while making her way over to Magnus with a large syringe in hand. "This'll only pinch a little if you just hold still dear..." She lowered the needle towards Magnus's neck.

"Don't you touch him!" Alec yelled from his place across the room. "If you hurt him I swear by the Angel I will kill you-" Alec was cut off abruptly when Clementine pressed on a remote that sent an electrical current zapping through his restraints. He let out one pain-filled cry before falling unconscious. With Magnus distracted Clementine took the opportunity to jam the needle into his neck. Magnus grew dizzy as he felt the blood being drained out of him and he fell back to his knees, the only thing holding him up were the chains around his wrists. His eyelids were heavy.

"It's okay dear, you can rest for now, the real fun won't start until later." The wicked woman said in a disturbingly soothing voice and Magnus blacked out.

*****************************

"Magnus!" He heard someone calling his name. "Magnus!" But he couldn't see them. "Magnus! Open your eyes baby please!" Oh, maybe that's why. Magnus's eyed fluttered open and he lifted his head to see that Alec was the one calling out for him. "Thank the Angel." Alec breathed in the reassurance that his husband was still alive.

"Alexander! Are you alright?" Magnus asked. Alec didn't have enough time to respond as Clementine reentered the room with a new cart of dastardly looking tools that she wheeled over to where Alec was being detained. "What are you doing?" Magnus inquired, standing.

"Creating my perfect little angel." She replied. "One with a little bit of the devil in it." With a wicked grin she hung a clear IV bag with dark red liquid inside, Magnus's blood, on the hook that loomed near Alec's head. She then took the IV tube and plunged the needle into the inside of Alec's elbow. Alec bared his teeth at her in response. As she went to start trickling the fluid into Alec's bloodstream, Magnus interjected.

"Please stop, that'll kill him!" He pleaded but Clementine did not care. She proceeded to smile at Magnus as she turned on the flow of his blood into Alec's arm. The instant Magnus's blood met his, Alec felt as if he were being burnt from the inside out. He hissed in pain but upon seeing Magnus's horrified look he said,

"I'm alright." He tried to keep the pain out of his voice, to be reassuring, but it must've not worked as Magnus's face only saddened further.

"Oh Maggie, look at him, putting on a brave face." Clementine mocked. "He is most definitely not fine. Your demonic blood running through him is causing his veins to alight with the heat of the fires of hell. Your blood. Your poison."

"No Magnus," Alec stopped her from speaking further. "This is NOT your fault. Don't go and blame yourself." Alec knew Magnus well enough to know that he would blame himself for any harm that would come to Alec.

"My my Magnus," Clementine chided. "I must say I'm quite impressed. You've picked a strong one. Most shadowhunters would be screaming out in pain right now while your beloved here is very calm. He's kept his breathing slow. Your venomous ichor hasn't reached his heart yet." For a moment she appeared to contemplate something until she continued, "I know exactly what'll speed this show along..." The look on her face was one Magnus and Alec both would see in their nightmares. She slowly strutted over to one of the tables with malicious looking devices, picking up a narrow, jagged knife. Smugly strolling back over to where Alec was restrained, she twirled the knife in her fingers. Alec kept his eyes deadlocked on Magnus. He knew what was about to happen. Taking the tip of the blade, Clementine gently touched it to the skin above Alec's left hip. She lightly dragged it upwards, drawing small traces of blood across his bare chest. Alec felt his heartbeat quicken in anticipation. When she reached just below his collarbone, she drove the blade in. Slowly. It cut through flesh and bone as dark crimson blood spilled from the wound. Alec was determined not to cry out, but as she violently twisted the knife and ripped it from where it was berried in his chest a roar of agony erupted from his lips. 

As more blood poured from the wound, Magnus couldn't help but notice it slowly blackening. When Magnus looked back to Alec's face he saw trickles of the black blood running from his nose and he began to cough violently, blood in his mouth.

"Ah looks like we're ready to begin!" Clementine clapped her hands, pleased.

 _Begin?_ Magnus thought horrified.


	7. 7: Last and First Breath

_**A/N: Hey y'all! Sorry it's been a while since my last update, it's the end of the semester sooo... yea I'll let that explain itself. Anyways, putting aside my unabating anxiety... here's the next chapter!!! <3** _

_***************** _

Magnus was terrified. He had never felt so afraid. Alec was dying. He always knew the day would come when he would have to watch his love die, but he thought they had more time. It wasn't supposed to end like this. "Please stop!" For the first time in his life, Magnus reduced himself to begging. "How do you expect to make him your perfect soldier when he's dead!" The smile on Clementine's face was sickening.

"Oh my, did I forget to tell you about that part? Oh well, better it be left a surprise anyways." She said with a wicked chuckle. There was a rattling sound as she clamored about with various beakers and bottles and flasks, each filled with a suspicious shade of liquid. At this point Alec's screams had ceased and each of his breaths were labored, his eyes only half open. Magnus's heart was tearing in two but his stomach churned when he saw the massive syringe Clementine wielded in her gloved hands. Snapping the rubber of her gloves she said, "This could get messy."

"Please, don't." Magnus's voice came out in a soft whisper, pleading with the last of his hope for mercy. Maybe she couldn't hear him. More likely she just didn't care. Clementine Morgenstern stalked toward Alec with the same cat-like grace of her brother, needle in hand, a look of excited determination on her face. As she grew nearer to the greatest love of his immortal life Magnus could do nothing but watch in horror as her long, slim fingers grasped the syringe and plunged it into Alec's abdomen, pushing the vibrant green sludge into his weak looking form.

Alec lay still for a moment, which felt like a million years to Magnus, and Clementine observed with anticipation. She looked practically giddy. Then Alec's body lurched on the table and a scream of pure agony tore through the chamber. Now shocked fully awake, Alec struggled against his restraints, eyes wide with fear. "MAGNUS!" His cries were desperate. Magnus tugged at his chains as hard as he could. They wouldn't budge.

"I'm here Alexander! I'm here!" He shouted. Alec whipped his head toward the sound, his eyes wild and searching.

"I can't see you!" Magnus had never heard such pain and terror in his husband's voice.

"It's okay, just listen to the sound of my voice!" Magnus tried to keep the waver out of his voice so that he could comfort his love but he was only able to just hold back his sobs.

"Magnus!" Alec's face twisted in pain and his back arched off the table.

"I'm right here my love, just hang on, it'll be all right!" Magnus knew that he was saying those words to himself as much as Alec.

"Oooo!" Clementine squealed with delight for some reason Magnus couldn't figure out. "It's happening!" She clapped her hands together as she ran back to grab a scalpel from the other table. She tightened the restraints around Alec's middle so that his writhing wouldn't disrupt her work and lowered the blade to his lower right abdomen and began slicing into the flesh. Her work was quick and shockingly gentle. The gaping hole in Alec grew wider and wider and soon Clementine pulled out Alec's appendix. Magnus thought to himself _All that just for his appendix?_

Then he saw it move. Clementine held it in her hands, gash in Alec's side pouring out black sludge, she was whispering words to it in a language he didn't understand. The lump thrashed in her hands and began to form limbs. Magnus could see arms and legs and a head growing out of the smooth tissues. Magnus stared in shock as a baby replaced what used to be one of Alec's organs. In his state of distress Magnus hadn't noticed Alec's moans grow softer and weaker. 

"Congratulations darlings," Clementine had a menacing silky tone to her voice. "It's a girl!" And with that, she disappeared, whisking away the baby.

Also disappearing, the link connecting Magnus's chains to the wall. He fell to the ground. His hands were still bound but he quickly got to his feet and ran to Alec's side. Alec was fluttering in and out of consciousness when her saw a blurred figure enter his vision. "Alexander!" He thought he heard someone calling his name, "Alexander!" It was Magnus. Alec held his eyes open while Magnus grasped his hand, his husband's free one attempting to stop the oozing of his wound.

"M-magnus," Alec's voice was low and raspy. Magnus's head snapped from Alec's bleeding stomach to those dark blue, ocean eyes that he loved so much to see Alec forcing a weak smile onto his face. "A-aku cinta k-kamu-" Alec's words were cut short, his hand limp in Magnus's.

And Magnus shattered...

He held Alec's lifeless body in his arms as violent sobs wracked his body. 

_Alexander. Not my Alexander._

**_A/N: THIS IS NOT THE ENDING! I just figured I'd make that extra clear cuz I'm not trying to break Y'all's hearts. well... maybe just a little... But anyway, there will be more, I just got filled with some new inspiration for where I wanna take this story and winter break is about to start so hopefully that means writing time! Anyways, thanks so much for reading! Questions and comments are always appreciated! <3_ **

**_~Nat_ **


	8. 8: Lost and Found

_**A/N:**_ _**AAAAAAAAH! SOOOO a lot happened in the last chapter! Sorry to leave y'all hanging like that! Anyways, this chapter starts at the institute...**_

"Magnus?!" Jace was running up and down the halls looking for his brother in law.

"He's not here Jace." The voice of Izzy rang through the halls. "Meet me in the control room!" The team(Jace, Izzy, Clary, Simon) all gathered. Jace was running his hands through his hair, he had already done so so many times that it was sticking straight up. Clary was twirling her stele nervously and Simon was tapping his foot while Isabelle stood solidly, hands pressed against the table, knuckles going white. "We need a plan." She said.

"I could try tracking him again. aha- AH!" Jace had fallen to the floor.

"Jace!" Clary started with concern, but she was interrupted by Isabelle.

"Is it Alec?!" She nearly shouted. All Jace could manage was a nod as he clutched his shoulder in pain. He writhed on the floor as the pain spread throughout his body, holding his stomach and coughing violently. In the midst of his suffering he had managed to get his shirt off and was desperately trying to get a look at his parabatai rune. Upon seeing the rune fade to near nothingness, Isabelle finally cracked. She screamed and ran for Jace when he went still. He was no longer feeling the pain, he was no longer feeling anything. He felt numb. An unimaginable emptiness seeped into his heart and he couldn't think of anything that could ever possibly fill that hole. Izzy was grasping him like he was her only lifeline. She had lost two of her brothers now. Alec had practically raised her and Jace, and Max... And now, he was gone.

There was a hissing noise in the air as Clary, who had been standing silently weeping, received a fire message.

_Greetings dear niece,_

_If you wish to see that warlock of yours and what's left of his lover ever again, you'll find them in the basement of your old apartment. Why am I telling you this? Well dear, I simply have no use for them anymore and I'm pretty sure if I leave them there the smell will draw in the stray dogs._

_With my deepest condolences,_

_Clementine Morgenstern_

Clary swallowed. "I know where they are. Magnus is with him." She said in a solemn tone. For the first time in minutes Jace stood up and said

"Then let's go get them." He sounded determined but the look on his tear streaked face was heartbroken.

**************************

There Magnus sat. In that cold, dark room. Holding onto Alec and the hope that in a few moments he might just open his eyes and Magnus would see those dark blue irises once again filled with life. But this would be futile. For like their adversary, Alec was gone. Beyond Magnus's reach.

A clanging sound could be heard from somewhere above and a light fell into the darkness. A figure dropped into the shadows and froze. The only identifying feature a tuft of golden hair that reflected what was left of the low light in the dank room. It was followed by another that spoke in a solemn voice.

"They're here." And with that piece of information two others leapt into the chamber.

"Magnus?" Clary's voice approached him. "Magnus what happened?" As she drew closer Magnus could see the silent tears streaking her face.

"He's gone." Magnus could still barely process the information. "He was b-bleeding out and there was n-nothing I could do." Soft sobs continued to reach the surface. Jace, who had been standing where he'd dropped into the room, started forward. His pace was slow and through his footsteps you could see the sorrow he trudged through. He reached Alec's limp form and brushed black curls out of the face of his lost parabatai.

"Let's bring him home." Jace couldn't keep the waver from his voice or the shakiness from his hands when he lifted Alec from Magnus's still chained arms and turned towards the exit. 

Clary placed an open rune onto Magnus's bindings and as the only thing that had stopped him from saving his greatest love clattered to the floor Manus once again broke down, but this time in rage. His anger seethed as his pent-up magic poured out of him, whirling, swirling around the dingy basement. The wind was a torrent of blue madness fueled by the warlock's regret for a life he will now never get to spend with his truest love, his inner thoughts wishing, pleading for another chance. He heard a voice calling to him through the tornado.

"Magnus!" Could it be? "Mags I'm here!" He saw a pale figure limping towards him. Magnus had never heard of such powerful acts of magic before. Could it be true? Had he done it? The wind died down and soon Magnus found himself in the embrace of a tall dark haired blue eyed shadowhunter. Magnus couldn't-wouldn't get his hopes up. He stood frozen there in his lover's arms.

"Alec?" He whispered.

"I'm here now. I'm really back. I'm gonna be okay. And I promise I'm never leaving you again." Alec responded. Magnus wrapped his arms around him so desperately you would think he was clinging to the air he needed to breathe. He nestled his face in the crook of the shadowhunter's neck and breathed in Alec's scent.

"Don't ever do that again." Magnus mumbled against Alec's skin, tears of happiness streaking through the dirt on the shadowhunter's chest.

"I don't plan on it." Alec looked down at his husband and smiled. Magnus returned the gesture. Alec was given a group hug by the gang and after they al climbed out of that musty hole, Magnus made a portal that led them back to the institute. Once there, Alec was struck y a suddenly all-consuming thought, he grabbed Magnus's arm.

"Alec? Is everything alright?"

"Magnus, the baby." Magnus's eyes widened at the thought. That child Clementine was wandering around with that she had created to be her perfect soldier was him and Alec's biological daughter. "We need to save our baby." The other's heard what he said and Jace- not knowing what had happened- began to say,

"It's okay, Max is with mo-" His speech was cut short when Alec collapsed onto the floor.


	9. The Search

**_A/N:_** **_Geez it's been awhile I had to re-read cuz I forgot my own exposition! XD and if you need a better explanation for Alec's revival, let's go with that he was only "Mostly dead" (Princess Bride rules)_**

Alec's eyes fluttered open and he found himself on a bed in the institute's infirmary, chatting seriously around him was Magnus, Jace, Isabelle, Clary, and Simon. Magnus had finished explaining all that had happened to the others **_(for the sake of the author's sanity)_** when Alec awoke, he struggled to sit up and Jace helped him while Magnus placed a copious amount of pillows behind him. His voice came out low and raspy when he spoke.

"We need to find her." Alec said to Magnus with pleading eyes to Magnus who responded with a soft nod.

"We will Alexander." Magnus's timbre held determination.

"Are you absolutely sure that this is even your kid? What if it's evil?" Simon, ever the cautioning one, asked.

"I heard the spell she used," Magnus replied. "it wasn't dark magic, and she may have some demon blood, but she also has angel blood." His voice was serious. "No one is born evil. And now, Clementine has our daughter." Magnus held Alec's hand. "And we're gonna take her back." Alec smiled at his husband. Magnus looked down at him. "But you need to recover first before you do anything. My magic may have brought you back to life but you just had an appendectomy. I'll start searching and if we haven't found her by the time you're better, then you can help. Until then, go back to sleep Alexander." Magnus spoke so lovingly that Alec reluctantly closed his eyes and drifted back to sleep. 

_(time skip brought to you by those annoying seagulls in Finding Nemo...)_

Magnus paced back and forth in the hall. He had absolutely no idea how to find clementine Morgenstern. Then it hit him. Clary. Clary and Clementine shared blood. (Also both their names start with Cl if we're pointing out similarities.) Blood tracking was stronger than typical warlock tracking so he rushed off to find the red headed niece of his nemesis.

Seeing as it was the middle of the night, Magnus knew exactly where Clary would be, the training room. Only because that's where Jace would be and Clary felt a need to help him decompress after the stresses he's been under the past few days. Jace was busy working off his emotions the only way he knew how, with a knife in his hand, so Magnus was able to catch Clary standing at the side of the room watching Jace. He drew her aside.

"I need your blood." Magnus stated bluntly. He didn't have the time nor the patience to deal with formalities or "Biscuit". Clary met his serious gaze with an equally confused one.

"What?" She asked. "Why?" Magnus sighed, she was wasting his time, so he spoke quickly.

"I need your blood to perform a more powerful tracking spell on Clementine, it has to be you since you're related by blood. Blood spells are more powerful yada yada can I please just have some of your blood so I can save my daughter form your witch of an aunt!" Magnus realized that he was yelling only after he had finished. Jace was now staring. Magnus took a deep breath. "I'm sorry Biscuit, I didn't mean to yell. I just really need your help." Clary's eyes were empathetic and she placed a hand on Magnus's arm.

"It's alright Magnus, I understand. Of course I'll help in whatever way I can." Magnus asked her to have a seat and he stuck the needle in her arm right then and there, unable to wait a second longer. He desperately needed to find his daughter, because if Alec continued stressing about it the way he was now, Magnus knew his recovery may not go as smoothly.

Once he had taken the sample he ran to Alec's office, where he'd been keeping his warlock-y stuff for when he needed it at the institute (which was often). He searched through his belongings for the spell and grabbed a map of New York, that's when Clary and Jace entered the room. Magnus prepared the spell by laying the map out on the desk and pouring the blood onto the center. The lights in the room seemed to dim as Magnus waved his hands through the air chanting the incantation, a breeze came out of nowhere and chilled the space. The wind rattled the walls as the chanting grew louder then all of a sudden... It stopped.

The room was dead still. Completely silent. Until Magnus took the map up into his hands and lit it on fire. "It didn't work!" Magnus was fuming. "She's blocking us from tracking her." Magnus slumped defeatedly into the desk chair then Jace spoke.

"So, Clementine's blocking herself from your tracking, but what about the kid?" Jace asked.

"What do you mean?" Clary was confused.

"If the baby is really Alec and Magnus's biological child then we could use their blood to track the her, shouldn't a parental bond be stronger to track than a niece?" Jace proposed and Magnus stood up and walked over to Jace and grabbed him by the arms.

"That's the smartest thing you've ever said. Let's go get Alec." Magnus let go of Jace and booked it out the door. Jace chose not to make a thing out of Magnus's comment and had to pretend not to be offended.

Alec was waking up just as Magnus reached the infirmary. He smiled at seeing his husband but was quickly confused by the look on his face. Magnus rushed into the room and produced a map of New York out of thin air. "Alexander how are you feeling?" Magnus asked.

"A bit better, I-" Was all Alec was able to get out before Magnus interrupted.

"I need some blood to track the baby." Magnus got straight to the point.

"Okay." Alec wasn't about to ask questions, he was as desperate as Magnus. Magnus pricked Alec's finger and dropped the blood onto the map.

"Hey I had to give way more blood." Clary asked with mock hurt in her voice.

"That's because you're a more distant relative to the one we were tracking." Magnus's patience was wearing thin and he pricked his own finger onto the map and began the spell, this time met with much less resistance, the drops of blood pooled together and trailed to a penthouse on 5th avenue. "We've got her."


End file.
